[English] 日本語
Yorodumi
- PDB-2ft3: Crystal structure of the biglycan dimer core protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ft3
TitleCrystal structure of the biglycan dimer core protein
ComponentsBiglycan
KeywordsSTRUCTURAL PROTEIN / SIGNALING PROTEIN / Proteoglycan / dimer interface
Function / homology
Function and homology information


A tetrasaccharide linker sequence is required for GAG synthesis / Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / ECM proteoglycans / transport vesicle / extracellular space / extracellular region
Similarity search - Function
Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine rich repeat ...Small leucine-rich proteoglycan, class I, decorin/asporin/byglycan / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Biglycan
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsScott, P.G. / Dodd, C.M. / Bergmann, E.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Biglycan Dimer and Evidence That Dimerization Is Essential for Folding and Stability of Class I Small Leucine-rich Repeat Proteoglycans.
Authors: Scott, P.G. / Dodd, C.M. / Bergmann, E.M. / Sheehan, J.K. / Bishop, P.N.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Biglycan
B: Biglycan
C: Biglycan
D: Biglycan
E: Biglycan
F: Biglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,84418
Polymers224,3826
Non-polymers2,46212
Water00
1
A: Biglycan
B: Biglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6156
Polymers74,7942
Non-polymers8214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Biglycan
D: Biglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6156
Polymers74,7942
Non-polymers8214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Biglycan
F: Biglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6156
Polymers74,7942
Non-polymers8214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.511, 119.222, 140.625
Angle α, β, γ (deg.)90.00, 116.61, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12B
22C
32D
42E
52F
13C
23D
33E
43F
14D
24E
34F
15E
25F
16A
26B
36C
46D
56E
66F
17B
27C
37D
47E
57F
18C
28D
38E
48F
19D
29E
39F
110E
210F
111A
211B
311C
411D
511E
611F
112B
212C
312D
412E
512F
113C
213D
313E
413F
114D
214E
314F
115E
215F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA25 - 28725 - 287
21ALAALAVALVALBB25 - 28725 - 287
31ALAALAVALVALCC25 - 28725 - 287
41ALAALAVALVALDD25 - 28725 - 287
51ALAALAVALVALEE25 - 28725 - 287
61ALAALAVALVALFF25 - 28725 - 287
12ALAALAVALVALBB25 - 28725 - 287
22ALAALAVALVALCC25 - 28725 - 287
32ALAALAVALVALDD25 - 28725 - 287
42ALAALAVALVALEE25 - 28725 - 287
52ALAALAVALVALFF25 - 28725 - 287
13ALAALAVALVALCC25 - 28725 - 287
23ALAALAVALVALDD25 - 28725 - 287
33ALAALAVALVALEE25 - 28725 - 287
43ALAALAVALVALFF25 - 28725 - 287
14ALAALAVALVALDD25 - 28725 - 287
24ALAALAVALVALEE25 - 28725 - 287
34ALAALAVALVALFF25 - 28725 - 287
15ALAALAVALVALEE25 - 28725 - 287
25ALAALAVALVALFF25 - 28725 - 287
16TYRTYRPROPROAA295 - 307295 - 307
26TYRTYRPROPROBB295 - 307295 - 307
36TYRTYRPROPROCC295 - 307295 - 307
46TYRTYRPROPRODD295 - 307295 - 307
56TYRTYRPROPROEE295 - 307295 - 307
66TYRTYRPROPROFF295 - 307295 - 307
17TYRTYRPROPROBB295 - 307295 - 307
27TYRTYRPROPROCC295 - 307295 - 307
37TYRTYRPROPRODD295 - 307295 - 307
47TYRTYRPROPROEE295 - 307295 - 307
57TYRTYRPROPROFF295 - 307295 - 307
18TYRTYRPROPROCC295 - 307295 - 307
28TYRTYRPROPRODD295 - 307295 - 307
38TYRTYRPROPROEE295 - 307295 - 307
48TYRTYRPROPROFF295 - 307295 - 307
19TYRTYRPROPRODD295 - 307295 - 307
29TYRTYRPROPROEE295 - 307295 - 307
39TYRTYRPROPROFF295 - 307295 - 307
110TYRTYRPROPROEE295 - 307295 - 307
210TYRTYRPROPROFF295 - 307295 - 307
111TRPTRPPHEPHEAA309 - 327309 - 327
211TRPTRPPHEPHEBB309 - 327309 - 327
311TRPTRPPHEPHECC309 - 327309 - 327
411TRPTRPPHEPHEDD309 - 327309 - 327
511TRPTRPPHEPHEEE309 - 327309 - 327
611TRPTRPPHEPHEFF309 - 327309 - 327
112TRPTRPPHEPHEBB309 - 327309 - 327
212TRPTRPPHEPHECC309 - 327309 - 327
312TRPTRPPHEPHEDD309 - 327309 - 327
412TRPTRPPHEPHEEE309 - 327309 - 327
512TRPTRPPHEPHEFF309 - 327309 - 327
113TRPTRPPHEPHECC309 - 327309 - 327
213TRPTRPPHEPHEDD309 - 327309 - 327
313TRPTRPPHEPHEEE309 - 327309 - 327
413TRPTRPPHEPHEFF309 - 327309 - 327
114TRPTRPPHEPHEDD309 - 327309 - 327
214TRPTRPPHEPHEEE309 - 327309 - 327
314TRPTRPPHEPHEFF309 - 327309 - 327
115TRPTRPPHEPHEEE309 - 327309 - 327
215TRPTRPPHEPHEFF309 - 327309 - 327

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
DetailsThe biological assembly is believed to be a dimer. The asymmetric unit contains 3 such dimers (chains A + B; chains C + D; chains E + F).

-
Components

#1: Protein
Biglycan / Bone/cartilage proteoglycan I / PG-S1 / Leucine-rich PG I


Mass: 37396.992 Da / Num. of mol.: 6 / Fragment: residues 38-369 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: Extracted from articular cartilage / References: UniProt: P21809
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M triammonium citrate, 20% (v/v) polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 3.4→22.9 Å / Num. all: 40497 / Num. obs: 40497 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.4→3.58 Å / % possible all: 97.7

-
Phasing

Phasing MRRfactor: 0.537 / Cor.coef. Fo:Fc: 0.225
Highest resolutionLowest resolution
Rotation4 Å22.84 Å
Translation4 Å22.84 Å
Phasing dmFOM : 0.72 / FOM acentric: 0.72 / FOM centric: 0.63 / Reflection: 36005 / Reflection acentric: 34907 / Reflection centric: 1098
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.7-22.8390.770.780.7214061299107
6.1-9.70.670.680.5747064504202
4.9-6.10.710.710.5560105816194
4.3-4.90.780.790.6961205946174
3.6-4.30.770.770.681106610793273
3.4-3.60.610.610.5966976549148

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XKU

1xku


Resolution: 3.4→23 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.786 / SU B: 30.915 / SU ML: 0.502 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2040 5 %RANDOM
Rwork0.258 ---
all0.259 42108 --
obs0.259 40497 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å22.49 Å2
2---0.85 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 3.4→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14512 0 162 0 14674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02215004
X-RAY DIFFRACTIONr_angle_refined_deg2.2761.98120337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93451815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.67324.256679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.929152683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8431596
X-RAY DIFFRACTIONr_chiral_restr0.1270.22293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211224
X-RAY DIFFRACTIONr_nbd_refined0.3130.37510
X-RAY DIFFRACTIONr_nbtor_refined0.360.59929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.5616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.3123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.55
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A20870.21
12B20870.16
13C20870.12
14D20870.1
15E20870.11
16F20870.1
21B20870.15
22C20870.11
23D20870.11
24E20870.09
25F20870.1
31C20870.1
32D20870.1
33E20870.09
34F20870.09
41D20870.08
42E20870.09
43F20870.08
51E20870.07
61A1060.29
62B1060.12
63C1060.13
64D1060.11
65E1060.1
66F1060.1
71B1060.11
72C1060.1
73D1060.1
74E1060.07
75F1060.09
81C1060.1
82D1060.09
83E1060.08
84F1060.08
91D1060.08
92E1060.08
93F1060.06
101E1060.06
111A1600.22
112B1600.17
113C1600.11
114D1600.14
115E1600.11
116F1600.12
121B1600.15
122C1600.1
123D1600.15
124E1600.09
125F1600.12
131C1600.11
132D1600.13
133E1600.09
134F1600.12
141D1600.12
142E1600.11
143F1600.1
151E1600.09
LS refinement shellResolution: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 126 -
Rwork0.328 2727 -
obs-2853 95 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more